keyword
MENU ▼
Read by QxMD icon Read
search

Bacterial whole genome sequencing

keyword
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#1
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223393/novel-bacterial-topoisomerase-inhibitors-with-potent-broad-spectrum-activity-against-drug-resistant-bacteria
#2
Cédric Charrier, Anne-Marie Salisbury, Victoria J Savage, Thomas Duffy, Emmanuel Moyo, Nathan Chaffer-Malam, Nicola Ooi, Rebecca Newman, Jonathan Cheung, Richard Metzger, David McGarry, Mark Pichowicz, Ralph Sigerson, Ian R Cooper, Gary Nelson, Hayley S Butler, Mark Craighead, Andrew J Ratcliffe, Stuart A Best, Neil R Stokes
The Novel Bacterial Topoisomerase Inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that do not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecules. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Gram-positive and Gram-negative pathogens, including biodefence microorganisms, and Mycobacterium tuberculosis No cross-resistance with quinolone-resistant Staphylococcus aureus and E...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28217117/the-promise-of-whole-genome-pathogen-sequencing-for-the-molecular-epidemiology-of-emerging-aquaculture-pathogens
#3
REVIEW
Sion C Bayliss, David W Verner-Jeffreys, Kerry L Bartie, David M Aanensen, Samuel K Sheppard, Alexandra Adams, Edward J Feil
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28213104/isolation-and-characterization-of-a-virulent-bacteriophage-infecting-acinetobacter-johnsonii-from-activated-sludge
#4
Niansi Fan, Rong Qi, Min Yang
A double-stranded DNA phage named AJO1, infecting Acinetobacter johnsonii, which plays an important role in wastewater treatment, was isolated from activated sludge in a full-scale municipal wastewater treatment plant. Based on morphological taxonomy, AJO1, with an icosahedral head 55 ± 2 nm in diameter and a non-contractile tail 8 ± 2 nm in length, was classified as a member of the Podoviridae family. Bacterial infection characteristics were as follows: no polyvalent infectivity, optimal multiplicity of infection of 10(-2); eclipse and burst size of 30 min and 51...
February 14, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28209394/ensifer-shofinae-sp-nov-a-novel-rhizobial-species-isolated-from-root-nodules-of-soybean-glycine-max
#5
Wen Hao Chen, Sheng Hui Yang, Zhao Hu Li, Xiao Xia Zhang, Xin Hua Sui, En Tao Wang, Wen Xin Chen, Wen Feng Chen
Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167(T) and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90...
February 2, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28207977/adaptation-of-the-pathogen-pseudomonas-syringae-during-experimental-evolution-on-a-native-versus-alternative-host-plant
#6
Sean Meaden, Britt Koskella
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species, and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also those experiencing opportunistic infections on novel hosts or that spill over among host populations...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#7
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#8
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28193166/vacsol-a-high-throughput-in-silico-pipeline-to-predict-potential-therapeutic-targets-in-prokaryotic-pathogens-using-subtractive-reverse-vaccinology
#9
Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali
BACKGROUND: With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28186143/the-first-complete-genome-sequences-of-the-aci-lineage-the-most-abundant-freshwater-actinobacteria-obtained-by-whole-genome-amplification-of-dilution-to-extinction-cultures
#10
Ilnam Kang, Suhyun Kim, Md Rashedul Islam, Jang-Cheon Cho
The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified or metagenome-derived genomes have been reported for the lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains, initially isolated by dilution-to-extinction culturing, eventually failed to be maintained as axenic cultures...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28183766/de-novo-whole-genome-sequence-of-xylella-fastidiosa-subsp-multiplex-strain-bb01-isolated-from-a-blueberry-in-georgia-usa
#11
Christopher Van Horn, Chung-Jan Chang, Jianchi Chen
This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%, 2,943 open reading frames (ORFs), and 48 RNA genes.
February 9, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28182785/virulence-and-immunogenicity-of-genetically-defined-human-and-porcine-isolates-of-m-avium-subsp-hominissuis-in-an-experimental-mouse-infection
#12
Nicolas Bruffaerts, Christelle Vluggen, Virginie Roupie, Lucille Duytschaever, Christophe Van den Poel, Joseph Denoël, Ruddy Wattiez, Jean-Jacques Letesson, David Fretin, Leen Rigouts, Ophélie Chapeira, Vanessa Mathys, Claude Saegerman, Kris Huygen
Mycobacterium avium subsp. hominissuis (Mah) represents a health concern for humans and to a lesser extent for pigs, but its zoonotic potential remains elusive. Using multispacer sequence typing (MST) we previously identified 49 different genotypes of Mah among Belgian clinical and porcine isolates, with 5 MSTs shared by both hosts. Using experimental intranasal infection of BALB/c mice, we compared the virulence and immunogenicity of porcine and clinical human isolates with shared genotype or with a genotype only found in humans or pigs...
2017: PloS One
https://www.readbyqxmd.com/read/28174306/a-mobile-element-in-muts-drives-hypermutation-in-a-marine-vibrio
#13
Nathaniel D Chu, Sean A Clarke, Sonia Timberlake, Martin F Polz, Alan D Grossman, Eric J Alm
: Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their mutation rates, but few mechanisms have been described for such modulation. Following experimental evolution and whole-genome resequencing of the marine bacterium Vibrio splendidus 12B01, we discovered one such mechanism, which allows this bacterium to switch to an elevated mutation rate...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28167561/functional-characterization-of-the-dna-gyrases-in-fluoroquinolone-resistant-mutants-of-francisella-novicida
#14
Yvan Caspar, Claire Siebert, Vivien Sutera, Corinne Villers, Alexandra Aubry, Claudine Mayer, Max Maurin, Patricia Renesto
Fluoroquinolone (FQ) resistance is a major health concern in the treatment of tularemia. With DNA gyrase described as the main target of these compounds, our aim was to clarify the contribution of both GyrA and GyrB mutations found in Francisella novicida clones highly resistant to FQs. Wild-type and mutated GyrA and GyrB subunits were overexpressed so that the in vitro FQ sensitivity of functional reconstituted complexes could be evaluated. Data obtained were compared with the MICs of FQs against bacterial clones harboring the same mutations and were further validated through complementation experiments and structural modeling...
February 6, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28166723/prophages-and-adaptation-of-staphylococcus-aureus-st398-to-the-human-clinic
#15
Seydina M Diene, Anna Rita Corvaglia, Patrice François, Nathalie van der Mee-Marquet
BACKGROUND: It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. RESULTS: Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28138508/data-on-gut-metagenomes-of-the-patients-with-alcoholic-dependence-syndrome-and-alcoholic-liver-cirrhosis
#16
Alexander V Tyakht, Veronika B Dubinkina, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitski, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun
Alcoholism is associated with significant changes in gut microbiota composition. Metagenomic sequencing allows to assess the altered abundance levels of bacterial taxa and genes in a culture-independent way. We collected 99 stool samples from the patients with alcoholic dependence syndrome (n=72) and alcoholic liver cirrhosis (n=27). Each of the samples was surveyed using "shotgun" (whole-genome) sequencing on SOLiD platform. The reads are deposited in the ENA (project ID: PRJEB18041).
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28131954/identification-and-initial-characterisation-of-a-protein-involved-in-campylobacter-jejuni-cell-shape
#17
Diane Esson, Srishti Gupta, David Bailey, Paul Wigley, Amy Wedley, Alison E Mather, Guillaume Méric, Pietro Mastroeni, Samuel K Sheppard, Nicholas R Thomson, Julian Parkhill, Duncan J Maskell, Graham Christie, Andrew J Grant
Campylobacter jejuni is the leading cause of bacterial food borne illness. While helical cell shape is considered important for C. jejuni pathogenesis, this bacterium is capable of adopting other morphologies. To better understand how helical-shaped C. jejuni maintain their shape and thus any associated colonisation, pathogenicity or other advantage, it is first important to identify the genes and proteins involved. So far, two peptidoglycan modifying enzymes Pgp1 and Pgp2 have been shown to be required for C...
January 25, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28118859/whole-genome-sequencing-reveals-high-resolution-epidemiological-links-between-clinical-and-environmental-klebsiella-pneumoniae
#18
Chakkaphan Runcharoen, Danesh Moradigaravand, Beth Blane, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Julian Parkhill, Narisara Chantratita, Sharon J Peacock
BACKGROUND: Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of K. pneumoniae, the evolution and clinical significance of environmental K. pneumoniae, as well as the relationship between clinical and environmental K. pneumoniae, are poorly defined...
January 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#19
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28112736/maturation-of-the-infant-microbiome-community-structure-and-function-across-multiple-body-sites-and-in-relation-to-mode-of-delivery
#20
Derrick M Chu, Jun Ma, Amanda L Prince, Kathleen M Antony, Maxim D Seferovic, Kjersti M Aagaard
Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers...
January 23, 2017: Nature Medicine
keyword
keyword
104574
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"